ABSTRACT Project 3 and is focused on defining immune regulatory genes and their functions that control West Nile virus (WNV) and Zika virus (ZV) infection using the Collaborative Cross (CC) mouse genetic system and human validation studies. WNV and ZV are emerging, neurotropic flaviviruses. WNV serves as a model flavivirus in mice, and we have developed novel CC mouse models of ZV infection. The CC recombinant inbred mouse panel encompasses >90% of all genetic diversity of the mouse genome and effectively models the genetic diversity found in the human population. Our Systems immunogenetics approach has identify quantitative trait loci (QTL) encoding immune-regulatory genes of WNV and ZV control. In this renewal application we will define these QTL and respective gene function in the immune regulation and control of WNV and ZV infection. Our studies of WNV infection reveal that unlike infection of inbred mice, the CC captures the full range of infection/disease outcomes found in humans, and can provide a ZV infection model in wild type CC mice. We screened 110 RI lines for WNV susceptibility and innate/adaptive immune phenotypes, from which we have linked disease and immune phenotypes to genotype. Our preliminary studies identify novel QTL encoding gene(s) linked to immune and disease phenotypes including innate and adaptive immune control of WNV and ZV susceptibility, infection in peripheral tissues, neuroinvasion, and CNS infection. Remarkably, this work reveals the Parkinson's disease gene, Park2, as an innate immune-regulatory gene that governs flavivirus infection. Our main hypothesis is that specific genes within these QTL function to control flavivirus infection and immunity. We will use our systems immunogenetics approach to investigate this hypothesis to define host genes regulating 1) innate immunity, and 2) adaptive immunity to flavivirus infection. Our study design is integrated into the larger U19 program to identify genes facilitated by the Mouse Models and System Genetics/Bioinformatics Cores. Genes we will be functionally validated in WNV and ZV infection studies, and assessed in SARS and influenza A virus studies of Projects 1 and 2) of human cells and targeted gene knockout mice to define immunoregulatory genes of virus infection.